Background: The modulation of mRNA levels across tissues and time is key for the establishment and operation ofthe developmental programs that transform the fertilized egg into a fully formed embryo. Although thedevelopmental mechanisms leading to differential mRNA synthesis are heavily investigated, comparatively littleattention is given to the processes of mRNA degradation and how these relate to the molecular programscontrolling development. Results: Here we combine timed collection of Drosophila embryos and unfertilized eggs with genome-wide microarray technology to determine the degradation patterns of all mRNAs present during early fruit flydevelopment. Our work studies the kinetics of mRNA decay, the contributions of maternally and zygoticallyencoded factors to mRNA degradation, and the ways in which mRNA decay profiles relate to gene function, mRNAlocalization patterns, translation rates and protein turnover. We also detect cis-regulatory sequences enriched intranscripts with common degradation patterns and propose several proteins and microRNAs as developmentalregulators of mRNA decay during early fruit fly development. Finally, we experimentally validate the effects of asubset of cis-regulatory sequences and trans-regulators in vivo. Conclusions: Our work advances the current understanding of the processes controlling mRNA degradationduring early Drosophila development, taking us one step closer to the understanding of mRNA decay processes inall animals. Our data also provide a valuable resource for further experimental and computational studiesinvestigating the process of mRNA decay.
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